Ask specific questions on how to do specific tasks in ApE

If people don't stop deleting text on these pages, I'm going to have to lock them. The idea is to leave text that others have written, so we can all benefit.

If you just want to send me a question, send it by email. Thanks.

I would like to automate plasmid sequencing data. Is there a way to run ApE scripts, or run specific tasks from command line?
  • there is a way to run scripts from within ApE. Press ctrl-0 (PC) or command-0 (apple). From there you can type or paste in Tcl scripts. You'll need to look at the source to see the names and parameters of the ApE procedures that you want to access. If you want help with that, let me know by email.

How do I run on Mavericks?
  • Download the Mavericks version of ApE.

Is there a way to adjust the linear map settings? I am trying to annotate a large Transposon and would like the map to wrap on the page instead of just being all scrunched together and not able to read.
  • In the enzymes menu of the sequence, you can set to "Selection only", then you can do a graphic map of sections at a time. Is that the kind of thing you are trying to do?
Yes that helps. On the map, is there a way to get the text (labels of ORFs etc) to be vertical?
  • There is no way to make vertical text at this time. Would you like the text rotated as a unit, or keep each letter upright and just put each letter on a new line? I probably won't implement it soon in either case, but curious what would be useful to people.

How to incorporate "already-made" annotation features of Genbank:
How to have ApE incorporate directly the gene annotations such as those present in genbank files.
for example, using
How to have all the genes appear as "colored "features" under ApE ?
  • Just open a genbank file that contains a DNA sequence (look at the end of the file to see if there's DNA in it). On the ncbi page linked, you have to click on "Show Sequence" on the right top side of the page. You can export that to a local file using the "Send" option at the top of the page. ApE should then be able to open it. ApE isn't designed for genome browsing, but as a plasmid editor, so you might not be able to browse as easily as you'd like on a giant sequence like this.

Is there a way to change the numbering? That is, instead of a sequence starting with number "1", could I set it to start at some other such as "8822"? Thanks!
  • Not at this time, sorry. It will be possible someday.

Helo. A question about Vector- Map Export: How can I export vector maps, so that the circle is in the middle of the map? Right now if I copy the Metafile, it depends on the length of the features I entered, where the middle of the vector circle ends up. At present I export the Metafiles into a presentation and modify the size and position of the exported vector maps until they end up aligned. Then I reexport from the presentation. This workaround is not very satysfying for I have quite a few more maps I would like to export. ... Thanks
  • if you don't resize the window, they will all be created with the same size circle. The circle only changes size when you resize the window. You can also set the circular map radius in preferences in v 2.0.13. As far as aligning the circle after you export a metafile- I'm not sure what you would like to happen. Of course the bounding box for the metafile is going to be at the edges of the objects in the metafile. This means that the circle position will be variable within the bounding box. ApE could make a blank box that is larger than any possible circular map and put it behind all of the metafile exports, but the box would have to be annoyingly big. Alternatively, you can scale the circle by 300% (or whatever size makes one corner outside the previous bounding box), then regroup the construct. You can then align the groups, and then reset the scale of the circle.

Hi, this may be a 'noob' ApE question. I am honestly not sure how to remove a colored "feature" from a DNA sequence after I add it. Can someone help? Thanks!
  • Go to the menu item Features>Edit Features. There you can change the stacking order and delete features in a sequence, and change the colors and type of individual features. If you are using the latest 2.0.x you can also edit the coordinates of the feature by adding or removing the currently selected region from hte feature.
    • Awesome, thanks so much!

Hello, how do you read the ORF graphic map? How to choose the right frame to translate? I am a little lost here... Thanks!
  • Met codons are short lines, stop codons are long lines. The top three lines are forward frames 0, 1, and 2. The bottom 3 lines are reverse frames. Someday I'll make the regions linked to the sequence, so you'll be able to click on a region and it'll select the region in the sequence.

Hi, How do I change the enzymes lists? I would like to use something other than the default list but I could not find the option to change in all of the menus. Thanks.
  • when you have the enzyme selector dialog open, you can use the menu item File>Open New Enzymes File. You can make new enzymes files by adding or removing enzymes- the easiest might be to open the All Enzymes file, deleting the ones that you don't want, then saving that set as your new enzymes file.

  1. How do I change the width of the feature arrow in a circular graphic map? Can I put the name of the feature inside the arrow?
  2. I can move the text in a graphic map by apple/drag, but can I change the orientation of the text? Can I delete the line connect the text and the circle?
  3. When I open the configure window for a graphic map, Config option 2, 3, 4 button don't do anything when I click them and there is no list in the Enymes and Features tab. Is this a bug or they have not been implemented yet?
I am using version 2.0.36e and Mac OS X 10.6.7.
  • The feature arrows are in the format x1 y1 x2 y2 ... xn yn. The Coordinates are relative to the width of the feature, centered on the feature, so 0 0 is at the end of the feature, in the middle of the line, 0 0.5 is at the top and 0 -0.5 is at the bottom. You can apple-drag them to any point, including inside the feature, but I haven't implemented moving the connector line to the inside of the feature- sorry.
  • You can't rotate the text at this time. That isn't possible in the version of Tcl/Tk that I'm using. It is in the latest beta versions, but the text still can't be copied or printed in rotated forms, so that's a big block to implementing rotated texts.
  • Enzymes and Feature configuration haven't been implemented yet- I should have taken them out of the interface.
I still don't quite understand the format of the arrow. My default numbers are 0 1 2 0 0 -1. Could you explain what each number means?
Also is it possible to move the feature text into the feature? like this
  • It is not possible to do rotated text at this time. The latest beta of Tcl/Tk just added rotated text, but printing and copying of text would also need to support it to make it feasible. Now that it's possible on the screen, copying and printing should follow eventually.
  • here are some more example arrows
  • #side arrow: 0 -1 1 0 .5 0 .5 1 -.5 1 -.5 0 -1 0
    #min arrow: 0 .5 1.5 0 0 -.5
    #half arrow: -.5 1 1 -.5 -.5 -.5
    #spike arrow:0 .5 -.5 1 -.5 1.1 1.6 0 -.5 -1.1 -.5 -1 0 -.5
    #fins: 0 .5 1 1.3 1 1 0 0 1 -1 1 -1.3 0 -.5
    #half block: 0 4 .3 4 .3 -.5 0 -.5
  • for a promoter, I use fwd arrow: 0 1 2 0 0 -1; rev arrow: 0 -.5 0 3 .2 3 .2 -.5, width 3
  • Untitled-1.gif
  • The default arrow: 0 1 2 0 0 -1
  • Untitled-2.gif

How do I create a group of enzymes to share?
If you are trying to make a groups file: in a text editor, make a file that consists of the name of the group, in quotations, a space, a brace {, a list of enzyme names case dependent, a brace }, a return character.
"My Lab Enzymes" {AatII BamHI EcoRI XbaI}

"The other lab's enzymes" {AvrII ClaI SpeI}

There is an example groups file in the default preferences, called "Supplier groups_12_05.txt"

Is there a way to allow multiple base pairs as possibilities in a search using alternate letters? Something like inserting an 'x' and allowing any base to appear there in the search.
Are you referring to the "Find" function? Yes. The find dialog accepts any of the degenerate base codes- you can search for AANTT, or AAWNSTT. You can also search for multiple patters by separating them with a semicolon or comma: "AANTT, AAWNSTT". You can also search with possible mismatches in the latest versions.

When I do an alignment or translation in APE, the result window is always too small. Is there a way to make this default window size bigger? or remember the window size I dragged the last time?
Are you referring to the width, or the font size?
You can set the font size in the preferences, you can set the width in the translate and align dialogs. (In align, you have to show alignment parameters first).

I am talking about the size of the window. I can change the line width, but not the width of the window. I want to set the height and width of the window.
I'll look into setting the widow size to the last size the window was made. This might not happen immediately.

After I select a short sequence from the sequence window, is there a way to highlight the selection?
If you want a temporary highlight, you can copy the sequence into a find then do highlight all. If you want it semi-permanently on the file, you can do Features>New Feature ("command-." using the keyboard). If you make a feature, you can set the direction and color, and it will show up in alignments (if you turn on copy highlighting in the alignment dialog) and graphic maps.

Can I request a new feature then? I want to make a temporary highlight, but don't want to use the find function. I simply want to highlight the selection I already made. Because if it is only one nucleotide, I cannot use the find function. Of course, a clear the highlight function would also be necessary.
If you can define how this isn't the add feature/delete feature, I'll consider this as a possible addition.

Because I don't want to define the selection as a feature. For example, I have a point mutation that I want to highlight in the sequence, then use it for sequence alignment so I can easily find the highlighted mutations in the alignment or translation.
Again, how is this different from defining the point mutation as a feature, then clearing the highlighting by deleting the feature when you are done? Making and deleting are easily accomplished by a right click in the sequence window. How is defining a feature not the same as highlighting a sequence region?

You are right. They are similar. Just that making a feature is not my first thought to highlight a sequence.

Is it possible to import features (oligos) from an excel file, using simply in each case the same forward and reverse colour?
Yes, you need to export the features as a tab delimited text. You need to specify the color for each, but you can just do a drag operation in Excel to copy the same color into each row.

If I add a new feature, would it be possible to directly add it in the feature list at the position you want it (so it is not added at the top and you have to use the lower button a lot of times)?
Not at this time, but that might be something I add in the future. You can push a feature to the bottom by right clicking on the feature name in the feature table at the top of the window, if that helps.

I can't seem to save features along with the data. I just started using ApE (ver 2.0.47 in Windows). An existing data file (*.str) was given to me and it contains cloned DNA in the plasmid DNA sequence. Several features are included. I lose all features when I doing any of the following: 1. Save non-modified data using a different *.str filename or a *.ape file. 2. Save modified data (i.e. features) using a new *.str filename as well as a *.ape file. Someone please help.
If you are still saving features, but you are losing the feature formatting, I suspect that your preferences have somehow been modified to turn on "Strict Genbank" formatting of saved files. Some other programs can't understand the formatting information included in an ApE formatted file, so strict genbank takes that extra information out. On the other hand, if you are completely losing the features, you may have set the default output format to Strider. Strider format files have no feature info in them at all.

I checked my Preferences: Default save file format is FASTA and default file extension is *.ape. I thought there might have been a problem installing ApE so I repeated the download/install. Same problem resulted. I also used a text editor to view the data files. Each file I saved, no matter the file format, have the FASTA format. The data.str file given to me (which contains feature formatting) did have additional info in the header. Something else happened that is strange: attempting to create a Autosave Directory in Preferences causes the program to freeze. I attempted this several times with the identical result.
Ok, there's your problem. FASTA files, like strider files, don't save feature information. You have to save as an APE-formatted file to save features. To do that, you have to set the preference for file saving file format to Ape, NOT FASTA. File extension is irrelevant to the situation, the format is set by the format preference and is not overriden by the extension. I don't know what's going on with the autosave. Where are you creating the directory- on a remote drive?

Only problem is that Preferences give me only 3 choices for Saving File Format: GenBank, Strider, and FASTA. New piece of information: On the Filetypes tab of Preferences is written in red exactly: ".ape is already: Unknown Program: MediaMonkey.APEFile". MediaMonkey is a program I use to manage music. Went to Windows Control Panel and associated *.ape files with A Plasmid Editor, not MediaMonkey. Then I rebooted and reinstalled ApE. When I checked Preferences in ApE, the same issues were presented and the same statement is present on the Filetypes tab. This is getting much too complicated.
Ok, sorry for the confusion, but ApE and Genbnank format are essentially the same. You want to save in Genbank format.

The extensions issue is entirely separate and shouldn't affect the format of the save at all. It doesn't really matter what extension you apply to your ApE files. It might be better to use something like .dna for your ApE files and let MediaMonkey use .ape. I don't know what alternate extensions MediaMonkey would be able to use, while ApE can use any number of others. I don't know why your reassociating of .ape to ApE didn't work. Reinstalling ApE might have let Media Monkey take control of the .ape extension. You shouldn't need to reinstall ApE and doing so will generally be a waste of time; ApE doesn't do a lot of jiggering with the system like other software, for which reinstalling can help. You might try reassociating then DON'T reboot or anything and just look back into the system and see if the reassociation is pointing to ApE.

Saving in GenBank format solved the problem - the feature info was maintained. Looks like today will be better than yesterday. Thank you for your attention and time.